Takashi Yokomori - Profile on Academia.edu (original) (raw)
Papers by Takashi Yokomori
Lecture Notes in Computer Science, Dec 1, 2003
Gene insertion and deletion are basic phenomena found in DNA processing or RNA editing in molecul... more Gene insertion and deletion are basic phenomena found in DNA processing or RNA editing in molecular biology. The genetic mechanism and development based on these evolutionary transformations have been formulated as a formal system with two operations of insertion and deletion, called insertion-deletion systems ([1], [2]). We investigate the generative power of insertion-deletion systems (InsDel systems), and show that the family INS 1 1 DEL 1 1 is equal to the family of recursively enumerable languages. This gives a positive answer to an open problem posed in [2] where it was conjectured to be negative.
This paper concerns a subdass of simple deterministic grammars, called very simple grammars, and ... more This paper concerns a subdass of simple deterministic grammars, called very simple grammars, and studies the problem of identifying the subclass in the limit from positive data. The class of very simple languages forms a proper subclass of simple deterministic languages and is incomparable to the class of regular languages. Besides some characterization results for very simple languages, we show that the dass of very simple grammars is polynomial time identifiable in the limit from positive data in the sense of Pitt. That is, there is an algorithm that, given the targeted very simple
arXiv (Cornell University), Jan 15, 2012
Reaction automata are a formal model that has been introduced to investigate the computing powers... more Reaction automata are a formal model that has been introduced to investigate the computing powers of interactive behaviors of biochemical reactions([14]). Reaction automata are language acceptors with multiset rewriting mechanism whose basic frameworks are based on reaction systems introduced in [4]. In this paper we continue the investigation of reaction automata with a focus on the formal language theoretic properties of subclasses of reaction automata, called linearbounded reaction automata (LRAs) and exponentially-bounded reaction automata (ERAs). Besides LRAs, we newly introduce an extended model (denoted by λ-LRAs) by allowing λ-moves in the accepting process of reaction, and investigate the closure properties of language classes accepted by both LRAs and λ-LRAs. Further, we establish new relationships of language classes accepted by LRAs and by ERAs with the Chomsky hierarchy. The main results include the following : (i) the class of languages accepted by λ-LRAs forms an AFL with additional closure properties, (ii) any recursively enumerable language can be expressed as a homomorphic image of a language accepted by an LRA, (iii) the class of languages accepted by ERAs coincides with the class of context-sensitive languages.
Proceedings of the 4th International Workshop on Algorithmic Learning Theory
Algorithmic Learning Theory, Nov 8, 1993
Note on the Equivalence Problem for a Class of Unary L-Systems
Transactions of the Institute of Electronics and Communication Engineers of Japan. Section E, 1981
DNA Computing: 12th International Meeting on DNA Computing, DNA12, Seoul, Korea, June 5-9, 2006, Revised Selected Papers (Lecture Notes in Computer Science)
Springer eBooks, 2007
Toward Soft Hardware
Soft Computing, Apr 1, 2001
... PaÆun, G. Rozenberg, A. Salomaa, DNA Computing. New Computing Paradigms, Springer, 1998, etc.... more ... PaÆun, G. Rozenberg, A. Salomaa, DNA Computing. New Computing Paradigms, Springer, 1998, etc.). Still, the papers by ``the Canadian team'' (L. Kari, R. Kitto, G. Gloor) and by ``the UK team'' (GG Owenson, M. Amos, DA Hodgson, A. Gibbons) are explicitly meant to explain ...
Algorithmic Learning Theory: 10th International Conference, ALT '99 Tokyo, Japan, December 6-8, 1999 Proceedings
... Series Editors Jaime G. Carbonell, Carnegie Mellon University, Pittsburgh, PA, USA Jorg Siekm... more ... Series Editors Jaime G. Carbonell, Carnegie Mellon University, Pittsburgh, PA, USA Jorg Siekmann, University of Saarland, Saarbrucken, Germany ... We are indebted to all members of the program committee: Nader Bshouty (Technion, Israel), Satoshi Kobayashi (Tokyo Denki ...
Learning Local Languages and its Application to Protein \alpha-Chain Identification
Hawaii International Conference on System Sciences, 1994
ABSTRACT
Learning local and recognizable Ω-languages and monadic logic programs
European Conference on Computational Learning Theory, Oct 27, 1994
We introduce two subclasses of regular !-languages called local !-languages and recognizable !-la... more We introduce two subclasses of regular !-languages called local !-languages and recognizable !-languages, and give two learning algorithms for those subclasses. We also relate these results to the learning problem for the class of monadic logic programs.
Corrigendum to “On the computing powers of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.svg"><mml:mi mathvariant="script">L-reductions of insertion languages” [Theor. Comput. Sci. 862 (2021) 224–235]
Theoretical Computer Science, Jun 1, 2022
The Computational Capability of Chemical Reaction Automata
Springer eBooks, 2014
We propose a new computing model called chemical reaction automata (CRAs) as a simplified variant... more We propose a new computing model called chemical reaction automata (CRAs) as a simplified variant of reaction automata (RAs) studied in recent literature ([7-9]).
arXiv (Cornell University), Nov 21, 2011
Reaction systems are a formal model that has been introduced to investigate the interactive behav... more Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that feature (string) language acceptors with multiset manipulation as a computing mechanism, and show that reaction automata are computationally Turing universal. Further, some subclasses of reaction automata with space complexity are investigated and their language classes are compared to the ones in the Chomsky hierarchy.
Proceedings of the 12th international conference on DNA Computing
On the Universality of Post and Splicing Systems
Machines, Computations, and Universality, 1998
ABSTRACT In search for a universal splicing system, in this paper we present a Post system univer... more ABSTRACT In search for a universal splicing system, in this paper we present a Post system universal for the class of Post systems, and we discuss its translation into an extended splicing system with multiplicity. We also discuss the complexity of the resulting universal splicing system, comparing our result with recent known results about the translation of universal Turing machines into splicing systems. 1 Introduction Since the possibility of molecular computing was shown by Adleman's pioneering work ([1]) which, in a test tube, experimentally solves a small instance of an NPcomplete problem, the theoretical formalization of such a new computing technology has been attracting much attention in computer science ([3][5][6][12][17]). One of the formal frameworks for molecular computations is the Tom Head's splicing system ( or H system ), which gives a theoretical foundation for computing based on DNA recombination. Tom Head's seminal work ([9]) on modeling DNA recombination as a splicing sys...
Hairpin Incompletion : An Extension of Bounded Hairpin Completion
arXiv (Cornell University), Feb 17, 2011
Hairpin completion and its restricted variant called bounded hairpin completion are operations on... more Hairpin completion and its restricted variant called bounded hairpin completion are operations on formal languages, inspired by a hairpin formation in molecular biology. We introduce a new operation of this kind, called {\it hairpin incompletion} which is in fact an extension of bounded hairpin completion. Further, the hairpin incompletion operation provides a formal language theoretic framework that models a bio-molecular technique nowadays known as Whiplash PCR. We study the closure properties of language families under both the operation and its iterated version. We show that a family of languages closed under intersection with regular sets, concatenation with regular sets, and finite union is closed under iterated hairpin incompletion, and that a family of languages containing all linear languages and closed under circular permutation, left derivative and substitution is also closed under iterated hairpin incompletion.
\mathcal {L}$$-reduction computation revisited
Acta Informatica, Mar 24, 2022
Proceedings of the 10th International Conference on Algorithmic Learning Theory
Journal of Robotics, Networking and Artificial Life, 2018
Natural computing (NC) is an emerging area of research that investigates computing techniques and... more Natural computing (NC) is an emerging area of research that investigates computing techniques and models inspired by nature on one hand, and it also investigates phenomena taking place in nature in terms of computational methodologies on the other hand. Thus, research in NC congenitally has interdisciplinary flavor, which bridges between computer science and various disciplines of natural science. Because of its interdisciplinary nature, NC connects and covers a broad spectrum of fundamental research fields including biology, chemistry, physics, medical science, and so forth. In this article, we give a concise introduction to the new computing paradigm of NC. Specifically, we give an overview of selected topics of the fields from theory to experiments, where the stress is primarily put on theoretical achievements in computing paradigms called molecular computing and chemical reaction computing.
Motivated by two notions of a reaction system ([3, 4, 5]) and a multiset ([1]), in this paper we ... more Motivated by two notions of a reaction system ([3, 4, 5]) and a multiset ([1]), in this paper we will introduce computing devices called reaction automata and show that they are computationally universal by proving that any recursively enumerable language is accepted by a reaction automaton. There are two points to be remarked: On one hand, the notion of reaction automata may be taken as a kind of an extension of reaction systems in the sense that our reaction automata deal with multisets rather than (usual) sets as reaction systems do, in the sequence of computational process. On the other hand, however, reaction automata are introduced as computing devices that accept the sets of string objects (i.e., languages over an alphabet). This unique feature, i.e., a string accepting device based on multiset computing in the biochemical reaction model can be realized by introducing a simple idea of feeding an input to the device from the : environment. :
Lecture Notes in Computer Science, Dec 1, 2003
Gene insertion and deletion are basic phenomena found in DNA processing or RNA editing in molecul... more Gene insertion and deletion are basic phenomena found in DNA processing or RNA editing in molecular biology. The genetic mechanism and development based on these evolutionary transformations have been formulated as a formal system with two operations of insertion and deletion, called insertion-deletion systems ([1], [2]). We investigate the generative power of insertion-deletion systems (InsDel systems), and show that the family INS 1 1 DEL 1 1 is equal to the family of recursively enumerable languages. This gives a positive answer to an open problem posed in [2] where it was conjectured to be negative.
This paper concerns a subdass of simple deterministic grammars, called very simple grammars, and ... more This paper concerns a subdass of simple deterministic grammars, called very simple grammars, and studies the problem of identifying the subclass in the limit from positive data. The class of very simple languages forms a proper subclass of simple deterministic languages and is incomparable to the class of regular languages. Besides some characterization results for very simple languages, we show that the dass of very simple grammars is polynomial time identifiable in the limit from positive data in the sense of Pitt. That is, there is an algorithm that, given the targeted very simple
arXiv (Cornell University), Jan 15, 2012
Reaction automata are a formal model that has been introduced to investigate the computing powers... more Reaction automata are a formal model that has been introduced to investigate the computing powers of interactive behaviors of biochemical reactions([14]). Reaction automata are language acceptors with multiset rewriting mechanism whose basic frameworks are based on reaction systems introduced in [4]. In this paper we continue the investigation of reaction automata with a focus on the formal language theoretic properties of subclasses of reaction automata, called linearbounded reaction automata (LRAs) and exponentially-bounded reaction automata (ERAs). Besides LRAs, we newly introduce an extended model (denoted by λ-LRAs) by allowing λ-moves in the accepting process of reaction, and investigate the closure properties of language classes accepted by both LRAs and λ-LRAs. Further, we establish new relationships of language classes accepted by LRAs and by ERAs with the Chomsky hierarchy. The main results include the following : (i) the class of languages accepted by λ-LRAs forms an AFL with additional closure properties, (ii) any recursively enumerable language can be expressed as a homomorphic image of a language accepted by an LRA, (iii) the class of languages accepted by ERAs coincides with the class of context-sensitive languages.
Proceedings of the 4th International Workshop on Algorithmic Learning Theory
Algorithmic Learning Theory, Nov 8, 1993
Note on the Equivalence Problem for a Class of Unary L-Systems
Transactions of the Institute of Electronics and Communication Engineers of Japan. Section E, 1981
DNA Computing: 12th International Meeting on DNA Computing, DNA12, Seoul, Korea, June 5-9, 2006, Revised Selected Papers (Lecture Notes in Computer Science)
Springer eBooks, 2007
Toward Soft Hardware
Soft Computing, Apr 1, 2001
... PaÆun, G. Rozenberg, A. Salomaa, DNA Computing. New Computing Paradigms, Springer, 1998, etc.... more ... PaÆun, G. Rozenberg, A. Salomaa, DNA Computing. New Computing Paradigms, Springer, 1998, etc.). Still, the papers by ``the Canadian team'' (L. Kari, R. Kitto, G. Gloor) and by ``the UK team'' (GG Owenson, M. Amos, DA Hodgson, A. Gibbons) are explicitly meant to explain ...
Algorithmic Learning Theory: 10th International Conference, ALT '99 Tokyo, Japan, December 6-8, 1999 Proceedings
... Series Editors Jaime G. Carbonell, Carnegie Mellon University, Pittsburgh, PA, USA Jorg Siekm... more ... Series Editors Jaime G. Carbonell, Carnegie Mellon University, Pittsburgh, PA, USA Jorg Siekmann, University of Saarland, Saarbrucken, Germany ... We are indebted to all members of the program committee: Nader Bshouty (Technion, Israel), Satoshi Kobayashi (Tokyo Denki ...
Learning Local Languages and its Application to Protein \alpha-Chain Identification
Hawaii International Conference on System Sciences, 1994
ABSTRACT
Learning local and recognizable Ω-languages and monadic logic programs
European Conference on Computational Learning Theory, Oct 27, 1994
We introduce two subclasses of regular !-languages called local !-languages and recognizable !-la... more We introduce two subclasses of regular !-languages called local !-languages and recognizable !-languages, and give two learning algorithms for those subclasses. We also relate these results to the learning problem for the class of monadic logic programs.
Corrigendum to “On the computing powers of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.svg"><mml:mi mathvariant="script">L-reductions of insertion languages” [Theor. Comput. Sci. 862 (2021) 224–235]
Theoretical Computer Science, Jun 1, 2022
The Computational Capability of Chemical Reaction Automata
Springer eBooks, 2014
We propose a new computing model called chemical reaction automata (CRAs) as a simplified variant... more We propose a new computing model called chemical reaction automata (CRAs) as a simplified variant of reaction automata (RAs) studied in recent literature ([7-9]).
arXiv (Cornell University), Nov 21, 2011
Reaction systems are a formal model that has been introduced to investigate the interactive behav... more Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that feature (string) language acceptors with multiset manipulation as a computing mechanism, and show that reaction automata are computationally Turing universal. Further, some subclasses of reaction automata with space complexity are investigated and their language classes are compared to the ones in the Chomsky hierarchy.
Proceedings of the 12th international conference on DNA Computing
On the Universality of Post and Splicing Systems
Machines, Computations, and Universality, 1998
ABSTRACT In search for a universal splicing system, in this paper we present a Post system univer... more ABSTRACT In search for a universal splicing system, in this paper we present a Post system universal for the class of Post systems, and we discuss its translation into an extended splicing system with multiplicity. We also discuss the complexity of the resulting universal splicing system, comparing our result with recent known results about the translation of universal Turing machines into splicing systems. 1 Introduction Since the possibility of molecular computing was shown by Adleman's pioneering work ([1]) which, in a test tube, experimentally solves a small instance of an NPcomplete problem, the theoretical formalization of such a new computing technology has been attracting much attention in computer science ([3][5][6][12][17]). One of the formal frameworks for molecular computations is the Tom Head's splicing system ( or H system ), which gives a theoretical foundation for computing based on DNA recombination. Tom Head's seminal work ([9]) on modeling DNA recombination as a splicing sys...
Hairpin Incompletion : An Extension of Bounded Hairpin Completion
arXiv (Cornell University), Feb 17, 2011
Hairpin completion and its restricted variant called bounded hairpin completion are operations on... more Hairpin completion and its restricted variant called bounded hairpin completion are operations on formal languages, inspired by a hairpin formation in molecular biology. We introduce a new operation of this kind, called {\it hairpin incompletion} which is in fact an extension of bounded hairpin completion. Further, the hairpin incompletion operation provides a formal language theoretic framework that models a bio-molecular technique nowadays known as Whiplash PCR. We study the closure properties of language families under both the operation and its iterated version. We show that a family of languages closed under intersection with regular sets, concatenation with regular sets, and finite union is closed under iterated hairpin incompletion, and that a family of languages containing all linear languages and closed under circular permutation, left derivative and substitution is also closed under iterated hairpin incompletion.
\mathcal {L}$$-reduction computation revisited
Acta Informatica, Mar 24, 2022
Proceedings of the 10th International Conference on Algorithmic Learning Theory
Journal of Robotics, Networking and Artificial Life, 2018
Natural computing (NC) is an emerging area of research that investigates computing techniques and... more Natural computing (NC) is an emerging area of research that investigates computing techniques and models inspired by nature on one hand, and it also investigates phenomena taking place in nature in terms of computational methodologies on the other hand. Thus, research in NC congenitally has interdisciplinary flavor, which bridges between computer science and various disciplines of natural science. Because of its interdisciplinary nature, NC connects and covers a broad spectrum of fundamental research fields including biology, chemistry, physics, medical science, and so forth. In this article, we give a concise introduction to the new computing paradigm of NC. Specifically, we give an overview of selected topics of the fields from theory to experiments, where the stress is primarily put on theoretical achievements in computing paradigms called molecular computing and chemical reaction computing.
Motivated by two notions of a reaction system ([3, 4, 5]) and a multiset ([1]), in this paper we ... more Motivated by two notions of a reaction system ([3, 4, 5]) and a multiset ([1]), in this paper we will introduce computing devices called reaction automata and show that they are computationally universal by proving that any recursively enumerable language is accepted by a reaction automaton. There are two points to be remarked: On one hand, the notion of reaction automata may be taken as a kind of an extension of reaction systems in the sense that our reaction automata deal with multisets rather than (usual) sets as reaction systems do, in the sequence of computational process. On the other hand, however, reaction automata are introduced as computing devices that accept the sets of string objects (i.e., languages over an alphabet). This unique feature, i.e., a string accepting device based on multiset computing in the biochemical reaction model can be realized by introducing a simple idea of feeding an input to the device from the : environment. :